Data from: Polymorphism pattern at a Miniature Inverted-repeat Transposable Element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

Unraveling the mechanisms involved in adaptation to understand plant morphological evolution is a challenging goal. For crop species, identification of molecular causal polymorphisms involved in domestication traits are central to this issue. Pearl millet, a domesticated grass mostly found in semi-arid areas of Africa and India, is an interesting model to address this topic: the domesticated form shares common derived phenotypes with some other cereals such as a decreased ability to develop basal and axillary branches in comparison with the wild phenotype. Two recent studies have shown that the orthologue of the maize gene Teosinte-Branched1 in pearl millet (PgTb1) was likely involved in branching evolution during domestication and that a Miniature Inverted-repeat Transposable Element (MITE) of the Tuareg family was inserted in the 3'-untranslated region of PgTb1. For a set of 35 wild and domesticated populations, we compared the polymorphism patterns at this MITE and at microsatellite loci. The Tuareg insertion was nearly absent in the wild populations, whereas a strong longitudinal frequency cline was observed in the domesticated populations. The geographic pattern revealed by neutral microsatellite loci clearly demonstrated that isolation by distance does not account for the existence of this cline. However, comparison of population differentiation at the microsatellite and the MITE loci and analyses of the nucleotide polymorphism pattern in the downstream region of PgTb1 did not show evidence that the cline at the MITE locus has been shaped by selection, suggesting the implication of a neutral process. Alternative hypotheses are discussed.解析植物适应相关机制以阐释植物形态演化，是一项极具挑战性的研究目标。对于作物而言，鉴定驯化性状相关的分子因果多态性，是该研究领域的核心议题。御谷（Pearl millet）是一类主要分布于非洲与印度半干旱地区的驯化禾本科作物，亦是探究该主题的理想模式物种：与野生型相比，驯化型御谷与其他部分谷类作物具有共同的衍生表型，例如基部分枝与腋生分枝能力下降。已有两项近期研究表明，御谷中玉米基因Teosinte-Branched1的同源基因PgTb1，可能在驯化过程中参与了分枝演化；且图阿雷格家族（Tuareg family）的微型反向重复转座元件（Miniature Inverted-repeat Transposable Element, MITE）已插入至PgTb1的3'非翻译区（3'-untranslated region）中。针对35个野生与驯化种群样本，本研究对比了该MITE位点与微卫星位点（microsatellite loci）的多态性模式。该图阿雷格转座元件插入在野生种群中几乎不存在，而在驯化种群中则呈现出显著的经度频率梯度分布。中性微卫星位点所揭示的地理分布模式清晰表明，距离隔离效应（isolation by distance）无法解释该梯度分布的成因。然而，对微卫星与MITE位点的种群分化（population differentiation）对比，以及对PgTb1下游区域的核苷酸多态性模式（nucleotide polymorphism pattern）分析，均未发现该MITE位点的梯度分布由选择作用塑造的证据，提示该过程属于中性演化过程。本研究对其他潜在假说展开了讨论。